RNA is less soluble in isopropanol so it will fall out of solution faster and cellular components like protein interact and creates a cloudy appearance.

Gel-like precipitation basically consists of RNA and few other residual cellular components.

Hi 

I use a protocol that uses those reagents and it seems to me you are not separating your RNA properly, therefore it is mixing with the DNA and cell debris. 

What I do is the following:

• Lyse my cells with trizol reagent and DIRECTLY to -80 degrees overnight. The longer the cells are in contact with the trizol, the worst RNA quality you would have, as the phenols on it decrease the purity.
• Next day, I defrost my trizol samples on ice (this is really important) and then I add the BCP. I shake the tubes, wait 10 minutes and centrifuge at 4 degrees. It is really important you use a cold centrifuge, ice temperatures prevents degradation of RNA
• after this centrifugation i get three phases. A pink one with proteins and cell debris, a gel-like one which is my DNA and a top clear one with is my RNA. This is the solution I take and transfer to new tubes, which then I wash with isopropanol and centrifuge in order to get my pellets. As the other researcher said, RNA pellets will precipitate in isopropanol solution, so then you can have your pellets. 

I think maybe you are getting some contaminants on your RNA and that's why it is getting cloudy. Also when I add the Isopropanol I always vortex my tubes and leave them for 10 minutes at room temperature. 

If you have more problems or questions I can handle my protocol to you, as I use trhe same reagents :) 

I have seen a similar phenomenon. There is likely to be RNA present but not of the quality or purity expected from a TRIzol extraction. TRIzol can be very reliable, producing excellent RNA yields. To achieve this, it is often worth being careful during the extraction process and leaving a small amount of the colourless, upper layer in place so as not to disturb the interphase. Perhaps 1/4 or 1/3 depending on the stability of the interphase layer. Disturbing the interphase is likely to be the source of any contamination. So leaving a little RNA behind to prevent this is usually preferential.  

Thank you all.

Actually, I leave 0.5 of the upper layer. usually, it was fine and i didn't have this problem before. As for the lysis stage, I used a protocol that says that i must rotate the tubes for at least 5 min on the rotator, and sometimes we even forget to stop the rotator and the purity was more then fine and also, i didn't see any cloudiness.

I'm asking because i isolate RNA using the same protocole i used many times, and it was fine. I just wonder if there are other possibilities- I read somewhere that the isopropanol might be the problem, is there any reason for that?

Hi Oron,

This is probably not relevant to you anymore, but perhaps for somebody else who comes to see this. I had a very similar issue couple of times. I have left a bunch of distance from my interphase while pipetting the aqueous layer. I am certain I didn't disturb the interphase while pipetting and yet I have tons of strange jelly like stuff when precipitating with isopropanol. However things are fine when I replace isopropanol with PEG. In my experience 30% PEG with 1.6M NaCl works well and I use 3 times the volume of aqueous phase (e.g. if you aq. phase is 0.5ml, I add 1.5ml PEG). This yields a nice pellet without any annoying jelly substance.